Putting a speedometer on a fish cladogram

If you think about it
fish swim in about three basic speeds: fast (like swordfish), slow (like sea horses) or they are bottom dwellers, sit-and-wait predators (like frogfish). We know some bottom dwellers eventually grew legs and became tetrapods. I hope you find this interesting as I apply colors according to fish speeds in this subset of the large reptile tree (LRT, 1548 taxa, Fig. 1), seeking phylogenetic patterns, if they exist.

Figure 1. Subset of the LRT focusing on basal vertebrates (fish) colorized according to speed/metabolism.

Not sure what else can be said here.
Evolution can take a bottom dweller and turn it into an open water speedster, but usually not the other way. The genus Seriola is an exception giving rise to mudskippers and frogfish. We are descendants of bottom dwellers. So are birds, bats and pterosaurs.

If any of the above generic names don’t ring a bell,
type them into the keyword search box.

 

Robustichthys: another nail in the coffin of the traditional clade ‘Holostei’

Updated May 3, 2020 with a new nesting for Robustichthys
with the armored catfish, Hoplosternum (Fig. 1).

Figure 1. Hoplosternum in vivo. You can see the armor/bone beneath its shiny skin. A sister to Robustichthys in the LRT.

We looked at the breakup of the traditional clade ‘Holostei’
earlier here. Today’s new taxon (Fig. 1) does not repair that breakup.

Figure 1. Robustichthys in situ.

Described as “the largest holostean of the Middle Triassic,”
Robustichthys luopingensis (Xu et al. 2014, Xu 2019; Figs. 1, 2) does not nest with other traditional holosteans in the large reptile tree (LRT, 1548/1680 taxa). Rather it nests with Pholidophorus (Fig. 3), a tuna-like fish from the Late Triassic. The skulls are nearly identical (Figs. 2, 3), more so that the two skulls attributed to Pholidophorus (Fig. 3). Adding colors to match tetrapod patterns (Fig. 2) is a practice I have encouraged all paleoichthyologists to adopt.

Figure y. Hoplosternum skull with bones identified as homologs to those in Robustichthys.

Figure z. Skull of Robustichthys and reconstruction of same. Note resemblance to Hoplosternum (Fig. y), distinct from diagram in Xu 2019.

Earlier the LRT nested
three traditional extant ‘holosteans’, Amia, the bowfin, the distinctly different Lepisosteus, the gar, and Pholidophorus (Fig. 3), from the Late Triassic, several nodes apart from one another (Fig. 4), creating a polyphyletic clade ‘Holostei’. Robustichthys nests with Pholidophorus. So traditional traits that describe members of the traditional clade ‘Holostei’ are convergent among ray-fin fish in the LRT, which tests skull and skeleton traits.

Xu 2019 only mentions Pholidophorus (while pulling a Larry Martin),
“Recently, Arratia (2013) described that the symplectic also articulates with the lower jaw in the pholidophorid Pholidophorus gervasutti, but this condition, unknown in other early teleosts, probably represents another convergent evolution.” Xu did not include the LRT sisters and cousins, Pholidophorus, Strunius, and Thunnus, among several other taxa that split gars from bowfins in the LRT. Neither did any of the prior workers who produced cladograms included in Xu 2019. So, taxon exclusion is once again the problem here. The only way to test convergence in evolution is to test it, not dismiss it, as Xu did.

What is a Symplectic?
“relating to or being a bone between the hyomandibular and the quadrate in the mandibular suspensorium of many fishes that unites the other bones of the suspensorium.”

Figure 4. Pholidophorus holotype from Arratia 2013, overlay drawing from Agassiz 1845.

Robustichthys luopingensis (Xu et al. 2014; Xu 2019; Middle Triassic) was described as the largest holstean fish of the Middle Triassic, but here the clade Holostei is polyphyletic and Robustichthys nests alongside the armored catfish, Hoplosternum. The long frontal extends posterior to the orbit. The expanded jugal is split up. The maxilla is absent, as in all catfish.

Figure 2. Subset of the LRT focusing on basal vertebrate (fish).

You may wonder
how the LRT is able to recover so many novel solutions that fall outside mainstream hypotheses. Evidently students and professors follow textbooks, the textbooks the professors write and update. The LRT confirms and/or refutes textbooks as it tests every possible combination of the 1548 taxa now employed. It does not matter that the multi-state character count is only a fraction of the taxon count. It does not matter if I do not see the specimen in person and use a professionally rendered drawing (Fig. 3).

What matters is taxon inclusion.
You can’t tell who is related to who else unless you invite them all to participate. That is the number one issue separating this growing online hypothesis of interrelationships and all others.

What matters is lumping and separating all tested taxa
to get a completely resolved tree and making sure that all sister taxa document a gradual accumulation of derived traits (which could include losses of certain bones or bone processes.

Reporting results that differ from the mainstream is not a crime
and does not injure reputations, in the long run. The competition is fierce for discoveries and those who invest heavily into their PhDs and the papers they write fear they have the most to lose. Contra this hypothesis, I’ve never seen a PhD pilloried for making a mistake (unless it was in a tent out in the field with a female student). So all you PhDs out there… relax. If you don’t want to fix the problems in our field of study by including a wider gamut of taxa, let the LRT do it.

As you’ll find out someday, some traditions and paradigms are wrong.
Don’t trust authority. Don’t trust the LRT. Find out for yourself which hypotheses are wrong and right by running your own tests. Let me know if you find a different tree topology than the LRT.

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References
Xu G-H 2019. Osteology and phylogeny of Robustichthys luopingensis, the largest holostean fish in the Middle Triassic. PeerJ 7:e7184 DOI 10.7717/peerj.7184
Xu G-H, Zhao L-J and Coates MI 2014. The oldest ionoscopiform from China sheds new light on the early evolution of halecomorph fishes. Biology Letters 10(5):20140204
DOI 10.1098/rsbl.2014.0204.

‘When whales walked: Journeys in Deep Time’ from PBS

PBS produced a nearly two hour dive into
various ‘new’ paleo-insights featuring many of paleontology’s rising stars and taxa. They called it, “When whales walked: Journey in Deep Time.” The photography and special effects were excellent. Trailer here.

The first chapter (crocs)
starts in Madagascar caves where Voay, the so-called ‘horned’ crocodile fossils are found (Fig. 1). Dr. Evon Hekkala uses DNA to chart croc evolution. Today only it’s cousin, the Nile crocodile, still lives in Madagascar.  (Surprised that Dr. Chris Brochu (U of Iowa) was not interviewed, since he has done so much work with these crocs.)

Figure 1. Dr. Evon Hekkala shows off a horned crocodile skull found in a Madagascar cave.

Chapter two (pre-crocs)
Dr. Bhart-Anjan Bhullar (Yale) takes us back to the Triassic, “in many ways the Age of Crocodiles”, as he assembles the bones of Poposaurus (Fig. 2). Preview here. Bhullar says, “These animals show us what crocodiles were like at the beginning of their evolution.” That’s close, but not true. Actually Poposaurus was basal to poposaurs and archosaurs (crocs + dinos), so it nests just outside of the croc clade. Junggarsuchus or Pseudhesperosuchus would have made his statement true, but he had Poposaurus in his cabinets at Yale. He also had another specimen, a real Triassic croc.

Figure 2. Revised skull reconstruction for the PEFO specimen. Here the anterior is considered a premaxilla. Those teeth are shaped like triangles, but they are very deeply rooted and exposed very little, which casts doubts on its hypercarnivory.

Continuing….
Bhullar next showed us a tiny ‘sphenosuchian’, nearly complete and nicknamed ‘little foot’ and cf. Dromicosuchus: YPM VP 57103). Originally it was discovered atop Popoposaurus.

Figure 3. The so-called ‘little foot’ specimen found with Poposaurus in Utah. YPM-VP-57103

Then Bhullar pulled a Larry Martin,
describing unique shared characters, rather than deciding what a croc is after phylogenetic analysis. We looked at YPM-VP-57103 earlier here.

Unfortunately,
Bhullar next held up a Euparkeria fossil and told viewers this specimen does not belong in the ancestry of crocs. That may be correct or incorrect depending on how you read it. According to the large reptile tree (LRT, 1546 taxa) Euparkeria nests so far back in the ancestry of crocs, it is too early to be a crocodylomorph.

Figure 4. YPM VP 057 103 reconstructed using color tracings from figures 1 and 2 in two scales. The smaller one shows the tail attached.

Chapter three (another croc)
Dr. Diego Pol (AMNH) presented a Jurassic notosuchid with a short snout and  large eyes on the side (not on the top). Pol discussed the variety of crocodylomorphs, but showed very few.

Chapter four (birds)
Dr. Julia Clarke (U of Texas) discussed birds and mentioned, “They can dive so deep into waters that light cannot reach.” Hmmm. Never heard that before. Clarke repeated the tradition based on genomic studies that half the total number of birds are passerines (song birds). By contrast, in the LRT sparrows (genus: Passer) give rise only to hoatzins, parrots and moas.

The PBS narrator noted that birds evolved from dinosaurs, then asked the silly question, “How could something so huge and heavy evolve into something so light?” According to the LRT, dinosaur taxa in the bird lineage were never huge, never heavy. Rather many basal small taxa gave rise to larger taxa—including moas and elephant birds, which are huge and heavy birds, as everyone knows. I just pulled a Larry Martin.

Chapter five (more birds)
Dr. Jacques Gauthier (Yale) said “Deinonychus altered everything we know about dinosaurs and birds” and that’s one of the major embarrassments according to Dr. John Ostrom, Gauthier’s mentor.  Gauthier mentions the first feathers were for warmth. Actually that was secondary. Warmth only happens when lots of feathers spread into a thick coat around the body. Gauthier describes the flight stroke of birds as they lift their forelimbs over the back, which is “very weird for tetrapods.” Gauthier makes no mention of Ken Dial‘s work or the elongation and locking down of the coracoids that enable a flight stroke in pterosaurs and birds.

Chapter six (more birds)
Dr. Jingmai O’Connor (USC, IVPP) describes dinosaurs buried in volcanic ash. Specimens document every stage of the dino–bird transition as they once lived side-by-side. She shows and discusses Caudipteryx, Jeholornis and Confuciusornis. O’Connor said an abbreviated tail evolved many times in dinosaurs and birds. You heard that here first, following a paper on pygostyles by O’Connor.

Chapter seven (more birds)
Dr. Erich Jarvis (The Rockefeller U) studies bird brains, learned behavior, and bird song evolution. The PBS narrator asks, “We all want to know is the bird family tree correct?” Jarvis says, he trusts genes to infer relatedness, and “most people trust DNA.” The LRT shows that “most people” are wrong. Jarvis thinks that “just a handful survived the (Cretaceous) mass extinction: shorebirds. ducks, geese, ostriches, emus.” This quietly omits one of the most highly derived bird clades, penguins in the Paleocene.

Chapter eight (whales)
Dr. Mark Uhen (George Mason U) mentioned that Charles Darwin suggested something like a bear could become a mysticete, then described a history of fossil whale discovery beginning with Basilosaurus, first thought to be a giant sea serpent.

Dr. Philip Gingerich (U Michigan) was highlighted for his discoveries in 1975, but even he made the mistake of assuming whale monophyly and descent from artiodactyls (a primitive deer). The LRT recovers at least two origins for extant whales where tenrecs nest basal to odontocetes and desmostylians nest basal to mysticetes. Gingerich discovered Pakicetus in Pakistan, which was once close to Madagascar, where tenrecs are found today.

Figure 5. At the Museum of Natural History in Paris, Dr. Christian De Muizon shows off the complete reconstruction of the Pakicetus skeleton, surprisingly an ancient relative of modern day whales.

Chapter nine (more whales)
Dr. Christian De Muizon (Muséum National d’Histoire Naturelle, Paris, Fig. 5) shows off a complete skeleton of Pakicetus, saying, “It looks like a dog with a long snout and webbed feet,” ignoring the fact that it looks more like a big tenrec and tenrecs echolocate.

Dr. Carlos Peredo (George Mason U) says baleen whales and toothed whales had their split early within cetacea (30 mya), in the descendants of Dorudon. By contrast, in the LRT the odontocete/mysticete split was much earlier, in the Jurassic. when tree shrews diversified.

Chapter ten (elephants)
Something about elephant tracks and extinction. Interesting to watch, but not much to comment about.

Simbakubwa: Not a giant carnivore. More like a hippo.

Borths and Stevens 2019 might have been confused by the giant canines
and giant molars of Simbakubwa (Fig. 1). The authors thought they were dealing with a giant carnivore related to hyaenodonts and creodonts (hence the title of their paper).

The large reptile tree (LRT, 1546 taxa) makes no assumptions. The LRT minimizes confusion by testing a wider gamut of taxa, including mesonychids (Fig. 2) and hippos. It turns out the great size of Simbakubwa is actually no big deal because it’s closer to hippos than lions. Most hippos are much bigger than most carnivores.

Figure 1. Simbakubwa from Broths and Stevens 2019, colors added, and compared to a lion mandible. Note the two medial views of the mandible with different shapes. Dorsal view of indented mandible and palate is similar to hippos.

Simbakubwa kutokaafrika (Borths and Stevens 2019; Miocene, 23mya; size; Fig. 1) was originally considered a gigantic carnivore, a member of the Hyaeondonta and Creodonta. Here it nests with Ocepeia (Fig. 3) as an offshoot of basal hippos with anteriorly placed eyes, convergent with carnivores, derived from mesonychids (Fig. 2).

Strangely
in dorsal view the mandible (dentary) was originally presented with an unnatural lateral kink/bend, creating a large open space where the teeth do not occlude. The authors report, “(dentary is reconstructed with the distal portion medially oriented out of natural position)“ and “the coronoid should be interpreted cautiously because it is reconstructed.”

Not sure why they published that mandible without fixing it. 
The authors note: “the tooth crowns are unworn”. Relative to the skull size, all the teeth were enormous and they extended far back in the skull. I note the shearing canines of extant hippos are already present here. It is also worthwhile to compare the only dentary premolar of Simbakubwa (Fig. 1) with the identical tooth found in the earlier mesonychid, Harpagolestes (Fig. 4). In any case, the suite to traits preserved nest Simbakubwa with mesonychid hippos, rather than hyaenodont creodonts (which are marsupials, not carnivores).

Hippos are not related to artiodactyls
in the LRT, contra the traditional myth. Hippo ancestors are basal to taxa leading to baleen whales. 

Figure 2. Mesonyx, the first known mesonychid was a sister to Hippopotamus in the large reptile tree. So maybe it was a plant eater, even though, like Simbakubwa, it looks like a predator with large lower canines.

Wikipedia reports,
“Simbakubwa, like other hyainailourids, probably was a specialist hunter and scavenger that preyed on creatures such as rhinoceroses and early proboscideans. It may have been somewhat less specialized in crushing bone than its later relatives such as Hyainailouros. However, like Hyainailouros, Simbakubwa possessed lingually rotating carnassial blades, ensuring a constant shearing edge throughout its life.” Hippos are also killers, but usually only for defense. They and all their sister taxa prefer plants.

Figure 3. Ocepeia: before and after. The original reconstruction is here compared to a tracing of CT scan, duplicated left to right.

Ocepeia daouiensis (Gheerbrant et al 2001, 2014; Paleocene, 60 mya; 9 cm skull length; Fig. 3) is a Hippopotamus ancestor derived from a sister to Merycoidodon. The original reconstruction was not an accurate representation of the fossil CT scan. The pneumatized skull contains many air spaces. The larger skulls have larger canines and so are considered male. The jugal deepens below the orbit, hiding the posterior molars in lateral view. The premaxilla is transverse. The upper canine rubs against the lower large incsior creating a facet, as in hippos and Harpagolestes (Fig. 4). Ocepeia was found with aquatic taxa and was probably amphibious.

Figure 4. Robust Harpagolestes nests between the hippos and Mesonyx. Note the identical lower premolar as in Simbakubwa (Fig. 1).

Several news organizations picked up on the sensational aspects
of this ‘gigantic carnivore’ discovery. Unfortunately, this may become embarrassing for the authors when confirmed.

The good news is:
we have more hippo and mysticete ancestors to study!

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References
Borths MR and Stevens NJ 2019. Simbakubwa ￿kutokaafrika, gen. et sp. nov. (Hyainailourinae, Hyaenodonta, ‘Creodonta,’ Mammalia), a gigantic carnivore from the earliest Miocene of Kenya. Journal of Vertebrate Paleontology e1570222 (20 pages) https://doi.org/10.1080/02724634.2019.1570222

wiki/Simbakubwa

https://www.ranker.com/list/killer-hippos-are-dangerous/mariel-loveland

https://www.washingtonpost.com/news/senegals-killer-hippo-problem/

http://blogs.discovermagazine.com/deadthings/2019/04/18/simbakubwa/#.XTX-IRTT63A

https://www.cbsnews.com/news/giant-lion-fossil-found-inside-drawer-at-kenyan-museum-2019-04-19/

Microdocodon: If those are hyoids, then where are the fingers?

A new mammaliaform, Microdocodon,
(Zhou et al. 2019; Figs. 1–4; Middle Jurassic, 165 mya) is exceptionally well preserved and complete, down to the smallest details. According to the authors, those details include “complex and saddle-shaped hyoid bones (Fig. 1), like those seen in modern mammals.”

Figure 1. From Zhou et al. 2019, colors added. Microdocodon is in yellow. The two taxa in gray are derived members of Glires and do not nest in the LRT where shown here. It is obvious from looking at this evolutionary progression that the two highly derived gnawing taxa do not document a gradual accumulation of derived traits, like the remaining plesiomorphic taxa do.

Timing?
Microdocodon was found in strata 40 million years into the Jurassic, some 40 million years after the appearance of the first mammal, Megazostrodon in the large reptile tree (LRT, 1545 taxa). Pre-mammal cynodonts lived alongside mammals throughout the Mesozoic.

H-shaped, articulated hyoids were unexpected in such a primitive cynodont
and a dozen news organizations picked up on the unexpectedness of this story. If valid this would suggest that a muscularized throat was present phylogenetically before the genesis of the milk-suckling clade, Mammalia.

Figure 2. Microdocodon throat region. Are those bones hyoids or fingers? If hyoids, then where are the fingers? Note the displaced radius (olive green)  reaching toward the throat. Only impressions of once present (or still buried) fingers are present on the right limb.

Unfortunately,
there may be reason to doubt the identity of these bones. Are they hyoids? Or fingers? If the mystery bones are indeed hyoids, then the fingers are missing. If fingers, then the hyoids are missing, which takes all the surprise and wonder out of the Zhou et al. paper.

FIgure 3. Microdocodon in situ. Plate and counter plate plus colors added. Manus, pelvis and pes reconstructed. The recombining of plate and counter plate is something that does not work as well in print.

From the abstract
“We report a new Jurassic docodontan mammaliaform found in China that is preserved with the hyoid bones. Its basihyal, ceratohyal, epihyal, and thyrohyal bones have mobile joints and are arranged in a saddle-shaped configuration, as in the mobile linkage of the hyoid apparatus of extant mammals. These are fundamentally different from the simple hyoid rods of nonmammaliaform cynodonts, which were likely associated with a wide, nonmuscularized throat, as seen in extant reptiles. The hyoid apparatus provides a framework for the larynx and for the constricted, muscularized esophagus, crucial for transport and powered swallowing of the masticated food and liquid in extant mammals. These derived structural components of hyoids evolved among early diverging mammaliaforms, before the disconnection of the middle ear from the mandible in crown mammals.”

The big question is:
If those are indeed hyoids, then where are the fingers? EVERYTHING else is present and visible on this perfectly preserved fossil, except, apparently, the fingers of both hands.

Further complication:
I looked closely at the purported hyoids and found they

1. included unguals
2. began at the wrist
3. were articulated like fingers
4. had all the proportions and correct number expected in a typical manus from that node on the LRT (Fig. 5).

Often enough,
when bones you expect are missing AND similar bones you don’t expect are present, you should suspect that a misidentification is taking place.

Figure 4. Microdocodon skull, plate and counter plate, colors added.

After phylogenetic analysis
Microdocodon nests at the base of the Tritylodontidae (Oligokyphus and kin) + (Riograndia + Chaliminia) clade. These are therapsids retaining a primitive quadrate/articular jaw joint, not like a mammal with a squamosal/dentary jaw joint.

At this point it is probably good to remember
that the most primitive mammals do not suckle. Prototherians, like echidnas and platypuses lick their mothers milk from sweat puddles on her belly. Only metatherians and eutherians have infants that suckle on their mothers’ teats, which is several nodes up the ladder from Microdocodon.

A docodont?
The authors considered Microdocodon a small member of the Docodonta, a clade traditionally defined by dental and mandible traits. Unfortunately, Microdocodon does not nest in the LRT with other clade members listed on the Wikipedia page. As we’ve seen many times, dental traits can converge.

The phylogenetic analysis of Zhou et al. employs “tritylodontids” as a suprageneric taxon nesting outside of Pachygenelus, (the opposite of the LRT) derived from Thrinaxodon and Massetognathus. To their peril, Zhou et al. include a long list of multituberculates, but no carpolestid and plesiadapid sister taxa recovered by the LRT. So taxon exclusion is a problem as highly derived multituberculates arise in Zhou et al. prior to primitive prototherians (Fig. 1). Also mis-nested in the Zhou et al analysis, the early and basal metatherian, Eomaia and the basal prototherian, Juramaia, nest as derived eutherians. These are all red flags, probably arrived at by an over-reliance on dental traits and the most typical problem in vertebrate paleontology: taxon exclusion. The LRT minimizes taxon exclusion because it tests such a wide gamut of taxa.

Figure 5. Microdocodon pectoral and forelimb reconstruction from DGS traced elements. Those fingers were originally considered hyoid elements. Yes, those are elongate coracoids, typically found in members of the Tritylodontidae.

But wait! All is not lost.
Microdocodon fills an important gap leading to the Tritylodontidae in the LRT. So it can still be exciting and newsworthy for this overlooked reason.

The pre-mammal/pre-tritylodontid split occurred
by the Middle Triassic, which gives Middle Jurassic Microdocodon plenty of time to evolve distinct traits. And it did. The snout is longer than typical. The medial metatarsals were atypically longer than the others. Tiny phalanges 3.2, 4.2, 4.3 and 5.2 reappear after disappearing several nodes earlier. That bit of atavism is interesting. The limbs are long and gracile with reduced interoseal space between the crural and ante brachial elements, mimicking/converging on more derived mammals.

Figure 6. Subset of the LRT focusing on basal Therapsida and Microdocodon’s nesting in it.

The authors report,
“Phylogenetically, Microdocodon and [coeval] Vilevolodon are the earliest-known mammaliaform fossils with mammal-like hyoids.” Vilevolodon is a highly derived, squirrel-like member of the clade Multituberculata within the rodent/rabbit clade of Glires within the Eutheria in the LRT.

Articulated hyoids
are exceptionally rare in the early fossil record of mammals. So are basal mammals.

Everyone is looking for a headline with every new fossil specimen.
Unfortunately, as we’ve seen time and again, you can’t believe everything you read, even after PhD peer review and publication in Nature and Science. Make sure you test all novel hypotheses with careful observation and a wide gamut phylogenetic analysis.

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References
Zhou C-F, Bullar B-A S, Neander AI, Martin T and Luo Z-X 2019. New Jurassic mammaliaform sheds light on early evolution of mammal-like hyoid bones. Science 365(6450):276–279.

https://www.sciencenews.org/article/flexible-bone-helps-mammals-chew-dates-back-jurassic-period

https://www.sciencedaily.com/releases/2019/07/190718140440.htm

For a dozen more popular articles: Google keyword: Microdocon.

 

Megistotherium: Not a gigantic hyaenodont creodont, a bear-dog marsupial

Updated April 5, 2022
with more taxa and revised scores.

Traditionally described as a gigantic hyaenodont creodont,
Megistotherium (Savage 1973; Miocene; Fig. 1) nests in the large reptile tree (LRT, 1544 taxa, then, 2070 taxa now) with the unnamed marsupial bear-dog, ‘not Amphicyon‘ (Fig. 2).

Figure 1. Megistotherium skull in several views. It is 2/3 of a meter in length. Don’t overlook the skull of tiny relative, Palaeosinopa with a 10cm skull length.

Figure 2. The unnamed marsupial bear-dog here labeled, ‘not Amphicyon’.

Megistotherium osteothlastes (Savage 1973; Miocene, 23mya; 66cm skull length) was originally considered a giant hyaenodontid creodont. Here it nests with the marsupial beardog ‘not Amphicyon‘. The jaw muscles were enormous. The large diameter canines were housed in large, laterally expanded maxillae. The braincase was narrow. In overall size and general features, Megistotherium is similar, by convergence, to the giant elephant shrew, Andrewsarchus.

Figure 1. Harpagolestes macrocephalus compared to sisters Sinonyx and Andrewsarchus to scale. Compare these elephant shrews to Megistotherium (Fig. 1)/

In the past,
several mammal taxa achieved gigantic proportions not found in today’s relatives.

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References
Savage RJ 1973. Megistotherium, gigantic hyaeonodont from Miocene of Gebel Zelten, Libya. Bulletin of the British Museum (Natural History) Geology 22(7):483–511.

wiiki/Megistotherium

Pappochelys: STILL not the ancestor of turtles, no matter what you read in Nature

Schoch et al. 2019 rehash an old trope.
suffering from overlooked taxon exclusion and convergence revealed by a wider gamut phylogenetic analysis, the large reptile tree (LRT, 1542 taxa).

From their abstract:
“Unlike any other tetrapod, turtles form their dorsal bony shell (carapace) not from osteoderms, but by contribution of the ribs and vertebrae that expand into the dermis to form plate-like shell components. Although this was known from embryological studies in extant turtles, important steps in this evolutionary sequence have recently been highlighted by the Triassic taxa Pappochelys, Eorhynchochelys and Odontochelys, and the Permian Eunotosaurus. The discovery of Pappochelys shed light on the origin of the ventral bony shell (plastron), which formed from enlarged gastralia. A major question is whether the turtle shell evolved in the context of a terrestrial or aquatic environment. Whereas Odontochelys was controversially interpreted as aquatic, a terrestrial origin of turtles was proposed based on evidence of fossorial adaptations in Eunotosaurus. We report palaeohistological data for Pappochelys, a taxon that exemplifies earlier evolutionary stages in the formation of the bony shell than Odontochelys. Bone histological evidence reveals (1) evolutionary changes in bone microstructure in ribs and gastralia approaching the turtle condition and (2) evidence for a predominantly amphibious or fossorial mode of life in Pappochelys, which support the hypothesis that crucial steps in the evolution of the shell occurred in a terrestrial rather than fully aquatic environment.”

Figure 1. Shoch and Sues compared Pappochelys to Odontochelys and Proganochelys, but deleted the more primitive Eunotosaurus. And it’s easy to see why. Eunotosaurus has wider ribs than its two purported successors. That and the LRT tell you its not a turtle, but a turtle mimic. Note the inaccuracy Schoch and Sues applied to their Odontochelys. The version from ReptileEvolution.com appears in frame 2 of this GIF animation.

We’ve explored such possibilities
earlier here, here and here. A wider gamut (1542 taxa) competing cladogram of vertebrate interrelationships recovers Pappochelys close to the ancestry of placodonts, and Eunotosaurus + Eorhynochelys close to Acleistorhinus. Neither are close to turtles. Odontochelys is close to the origin of soft shell turtles. The small horned pareiasaur, Sclerosaurus, is closer. Proganochelys is close to the origin of hard shell turtles. Meiolania and the small horned pareiasaur, Elginia, are closer. Convergence and taxon exclusion seem to be the trouble here.

Figure 2. Another gap is filled by nesting E. wuyongae between Bunostegos and Elginia at the base of hard shell turtles in the LRT.

Back to the Schoch et al. question:
“A major question is whether the turtle shell evolved in the context of a terrestrial or aquatic environment.” 

Answer:
Both. See dual origin of turtles from pareiasaurs and notes above. Schoch et al. are not working within the correct phylogenetic context. When they get the same results while including the turtle ancestors recovered by the wide gamut LRT, let me know. For now, apparently, they appear to be content to play in their little corner ignoring data that has been online for several years.

See and read:
https://www.researchgate.net/publication/328388481_The_dual_origin_of_turtles_from_pareiasaurs

Online cladogram here:

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References
Schoch RR, Klein N, Scheyer TM and Sues H-D 2019. Microanatomy of the stem-turtle Pappochelys rosinae indicates a predominantly fossorial mode of life and clarifies early steps in the evolution of the shell. Nature Scientific Reports 9:10430 online here

 

The flying fish (Exocoetus) enters the LRT alongside the rudder fish

Updated February 4, 2021
with the addition of taxa, Exocoetus nests with Seriola sonata, the rudder fish.

Updated again August 31, 2023
with the addition of Oreochima (Fig 1), a Late Jurassic flying fish and Opah (Fig 1) ancestor.

Figure 1. The origin of flying fish and opahs from smaller extant Danio and Late Jurassic Oreochima AMNH 9910. The broken ascending process of the preopercular (light yellow) is restored here.

Exocoetus volitans (Linneaus 1758; up to 30m ) is the extant blue flyingfish, here related to the swordfish, Xiphias. Exocoetus travels in schools or schoals. Sometimes they exit the water to avoid predators. Juveniles have a relatively shorter torso. Hatchlings are slow-moving and tiny. Note the antorbital fenestra and large lacrimal, as in Xiphias. Distinctly flying fish have a jaw joint directly below the orbit. The coracoid is larger than the scapula, raising the pectorl fins.

Seriola zonata (Valenciennes 1833; commonly 50cm, up to 75cm) is the extant banded rudderfish. Large individuals (over 10 inches) have no abdominal bands,  but a raccoon-stripe on the eye and an iridescent gold stripe on the side are present. Adults are usually called amberjacks. Striped juveniles are usually called pilotfish. This generic fish is basal to a wide variety including flying fish, puffers, frogfish, anglers and mudskippers.

If I missed a citation that predates this one
that supports this hypothesis of interrelationships, please send me the citation. It does not appear to be matched by genomic (gene/molecule) studies.

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References
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Valenciennes A in Cuvier G and Valenciennes A 1833. Histoire naturelle des poissons. Tome neuvième. Suite du livre neuvième. Des Scombéroïdes. 9: i-xxix + 3 pp. + 1-512. Pls. 246-279.

wiki/Exocoetus_volitans
wiki/Seriola
wiki/Amberjack

Testing for bipedalism in archosaurs (and pterosaurs)

Grinham, VanBuren and Norman 2019
looked at the origin of bipedalism in the archosaur and pre-archosaur ancestors of birds.

They report, “We test whether facultative bipedality is a transitionary state of locomotor mode evolution in the most recent early archosaur phylogenies using maximum-likelihood ancestral state reconstructions for the first time. Across a total of seven independent transitions from quadrupedality to a state of obligate bipedality, we find that facultative bipedality exists as an intermediary mode only once, despite being acquired a total of 14 times. We also report more independent acquisitions of obligate bipedality in archosaurs than previously hypothesized, suggesting that locomotor mode is more evolutionarily fluid than expected and more readily experimented with in these reptiles.”

The authors used the cladograms of Ezcurra 2016 and Nesbitt 2011,
both of which are riddled with inappropriate taxon inclusion and exclusion problems as reported earlier here and here. Therefore comparisons regarding the number of times obligate bipedality in archosaurs occurred is useless lacking a consensus phylogenetic contaxt. In the large reptile tree (LRT, 1542 taxa) bipedality occurs only once in archosaurs. It just precedes the origin of the archosaurs (crocs + dinos only). Ezcurra, Nesbitt and Grinham et al. include a long list of inappropriate taxa in their inclusion set according to the LRT that skews results (e.g. the lepidosauromorphs: Jesairisosaurus, Macrocnemus, Mesosuchus, Gephyrosaurus, Planocephalosaurus, Eudimorphodon, Dimorphodon).

Grinham, VanBuren and Norman 2019
follow Nesbitt 2011 who listed the pterosaurs Eudimorphodon and Dimorphodon as archosauriforms. Grinham et al. 2017 considered both to be quadrupeds without explanation. The only pterosaur paper cited by Grinham et al. is Padian 2008. Peters 2007 recovered pterosaurs with lepidosaurs like Huehuecuetzpalli, later validated, expanded and published online in LRT. Peters 2000, 2011 reported on bipedal pterosaur tracks and restricted most cited pterosaur ichnites to flat-footed beach-combing pterosaur clades. Use keyword “bipedal pterosaur tracks” in the SEARCH box to see prior samples of digitigrade and bipedal tracks reported by this blogpost along with their citations.

Padian 2008 reported
“Peters (2000) also reached the conclusion that pterosaurs were not ornithodirans, and found instead that they were nested within what is traditionally considered the Prolacertiformes. It remains to be seen whether other workers can duplicate this result, but a recent analysis by Hone and Benton (2007) failed to find support for Peters’ analyses. For the present, because five different analyses have found that pterosaurs are ornithodirans, and the systematic community seems to have largely accepted this, the present paper will proceed with this provisional conclusion, without discounting other possible solutions.”

We looked at the bogus results
of Hone and Benton 2007 earlier here. They dropped taxa proposed as pterosaur ancestors by Peters 2000 because their inclusion would have tilted their supertree toward the topology recovered by Peters 2000, who tested four previously published cladograms by adding novel taxa to them. One year earlier than Peters 2000, co-author Benton 1999 had proposed Scleromochlus as a pterosaur sister/ancestor, which Peters 2000 invalidated. Evidently professor Benton did not appreciate that and succeeded, at least in Padian’s eyes, to dismiss Peters 2000 as an unacceptable and suppressible minority view.

Note that none
of Padian’s “five different analyses” used novel taxa proposed by Peters 2000. Padian’s report, “The systematic community seems to have largely accepted this,” demonstrates that Padian and his community were adverse to testing the novel taxa of Peters 2000 on their own terms, preferring the cozy comfort of tradition and orthodoxy — and they did this after Peters 2000 invalidated earlier efforts simply by adding a few taxa. Very easy to do. Even today it remains impossible to explain the origin of pterosaurs as archosaurs in a phylogenetic context because they are not archosaurs. In the world of academics, taxon exclusion remains a useful tool. We should all fight against this practice.

Later Padian 2008 reports, 
“Alternatively, if we consider that pterosaurs evolved from quadrupedal basal archosauromorphs such as Prolacertiformes (Peters, 2000), a rather different model of limb evolution must be proposed. In prolacertiforms the humerus is longer than the forearm and the femur is longer than the tibia; the glenoacetabular length is also long, as in most terrestrial quadrupeds. To attain the proportions seen in basal pterosaurs, the relative lengths of humerus and forearm and of femur and tibia would have to have been reversed, and the vertebral column would have had to shorten considerably (or the limb segments increase). These changes are independent of the extensive reorganization of the joints for erect posture and parasagittal gait, for which there is no evidence so far in prolacertiforms.”

Figure 1. Click to enlarge. The origin of the pterosaur wing and the migration of the pteroid and preaxial carpal. A. Sphenodon. B. Huehuecuetzpalli. C. Cosesaurus. D. Sharovipteryx. E. Longisquama. F-H. The Milan specimen MPUM 6009, a basal pterosaur.

Note: Padian 2008 chose to ignore the limb proportions
of Longisquama (Figs. 1, 2) another taxon proposed by Peters 2000 with a humerus shorter than the forearm, as in pterosaurs. He also ignored Sharovipteryx, another taxon proposed by Peters 2000, with a femur shorter than the tibia. In the world of academics, taxon exclusion remains a useful tool. We should all fight against this.

Padian 2008 also chose to ignore the evidence for bipedalism
in Cosesaurus (Fig. 2) matching facutatively bipedal Rotodactylus tracks (Peters 2000) and Sharovipteryx (Fig. 2), an obligate biped based on proportions. Both have the short torso relative to the limb length sought for and purposefully overlooked by Padian 2008 (see above quotation). In the world of academics, taxon exclusion remains a useful tool. We should all fight against this.

Figure 2. The origin of pterosaurs now includes Kyrgyzsaurus, nesting between Cosesaurus and Sharovipteryx.

Students of paleontology:
I’m sorry, this is just the way it is.

Getting back to bipedalism in archosaurs,
the LRT, subset Fig. 4) documents the patterns and possibilities of bipedal locomotion in taxa preceding dinosaurs. The topology here employs more taxa, pushes pterosaurs over to lepidosaurs (Peters 2007) and nests only Crocodylomorpha + Dinosauria within the Archosauria. Poposauria is the proximal outgroup. This is where bipedalism in archosaurs first appeared. Other bipedal taxa achieved this ability by convergence. Secondary quadrupedalism occurred several times in archosaurs, and by convergence in certain derived pterosaurs (e.g. ctenochasmatids and azhdarchids), as evidenced by their backward pointing manual digit 3 in ichnites.

Figure 3. Subset of the LRT focusing on the archosauromorph synapsid-grade taxa and diapsid-grade taxa with color added to bipedal taxa.

As documented here and elsewhere
It does not matter if certain hypotheses are peer-reviewed and published or not.
Academic authors can choose to omit pertinent taxa and papers knowing that ‘friendly’ academic referees and editors will likewise choose to overlook such omissions. Apparently all academics seek and work to maintain the orthodox line, no matter how invalid it may be.

That’s why this blogpost and ReptileEvolution.com came into being.
We’re talking about hard science. Ignoring and omitting hard evidence cannot be tolerated or coddled. I ask only that academic workers rise to the professionalism they seek to inspire in their own students. History will put this all into perspective. Professional legacies may end up in shame unless they take action soon. Just test the taxa. 

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References
Benton MJ 1999. Scleromochlus taylori and the origin of the pterosaurs. Philosophical Transactions of the Royal Society London, Series B 354 1423-1446. Online pdf
Ezcurra MD 2016 The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriforms. PeerJ 4, e1778. (doi:10.7717/peerj.1778)
Grinham LR, VanBuren CS and Norman DB 2019. Testing for a facultative locomotor mode in the acquisition of archosaur bipedality. R. Soc. open sci. 6: 190569. http://dx.doi.org/10.1098/rsos.190569
Hone DWE and Benton MJ 2007. An evaluation of the phylogenetic relationships of the pterosaurs to the archosauromorph reptiles. Journal of Systematic Palaeontology 5:465–469.
Hone DWE and Benton MJ 2008. Contrasting supertree and total evidence methods: the origin of the pterosaurs. Zitteliana B28:35–60.
Nesbitt SJ 2011. The early evolution ofArchosaurs: relationships and the origin of major clades. Bull. Am. Museum Nat. Hist. 352, 1–292. (doi:10.1206/352.1)
Padian K 2008. Were pterosaur ancestors bipedal or quadrupedal? Morphometric,
functional, and phylogenetic considerations. Zitteliana R. B Abhandlungen der Bayer.
Staatssammlung fur Palaontologie und Geol. 28B, 21–28.
Peters D 2000a. Description and Interpretation of Interphalangeal Lines in Tetrapods.  Ichnos 7:11-41.
Peters D 2000b. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.
Peters D 2002. A New Model for the Evolution of the Pterosaur Wing – with a twist. – Historical Biology 15: 277–301.
Peters, D 2007. The origin and radiation of the Pterosauria. Flugsaurier. The Wellnhofer Pterosaur Meeting, Munich 27
Peters D 2011. A Catalog of Pterosaur Pedes for Trackmaker Identification. Ichnos 18(2):114-141. http://dx.doi.org/10.1080/10420940.2011.573605

Indrasaurus and Microraptor: the inside story

Updated July 7, 2020
the LRT moves Meyasaurus, Indrasaurus and Hoyalacerta to the base of the Yabeinosaurus + Sakurasaurus clade within the Scleroglossa and Squamata.

O’Connor et al. 2019 report on
a small pre-squamate lizard, Indrasaurus wangi (Fig. 1; STM5-32), ingested just before the untimely death of its feathered predator, Microraptor (Fig. 3, STM5-32). Both were added to the large reptile tree (LRT, 1542 taxa). O’Connor et al. note, “This is the fourth specimen of Microraptor described with ingested remains preserved in the abdominal cavity, with enantiornithine birds, mammals, and fish previously documented.”

Figure 1. Indrasaurus reconstructed. Sister taxa do not have an antorbital fenestra, so the one that appears here is suspect, but possible.

From their abstract:
“Phylogenetic analysis suggests Indrasaurus wangi gen. et sp. nov. is a basal scleroglossan closely related to the slightly older Liushusaurus. Comparison of ingested remains preserved across Paraves suggests that dromaeosaurids retained the plesiomorphic condition in which ingested prey were fully digested, rather than egested, as has been demonstrated was the case in the probable troodontid Anchiornis.”

In the LRT Liushusaurus is an outgroup taxon to the Squamata, a clade defined by extant taxa. Liushusaurus nests six nodes apart from Indrasaurus.

Figure 2. Hoyalacerta in situ nests close to Indrasaurus in the LRT. Note the similarly long torso and short, small limbs.

O’Connor et al. remarked,
“Phylogenetic relationships in fossil squamates are difficult to determine with currently available matrices. Given the uncertainty regarding squamate relationships at this time, we do not find it unusual that our results add to the current disparity.” O’Connor et al. did not realize the clade Protosquamata enclosed the clade Squamata. The LRT was the first to recover this clade and another previously overlooked lepidosaur clade, the Tritosauria, nesting between Sphenodontia and Squamata.

Figure 3. Indrasaurus and Microraptor to scale. Despite what appear to be jaw tips, those are separated dentaries an the skull is preserved in dorsal view, lacking premaxillae and nasals.

In the LRT,
Indrasaurus (STM5-32) nests close to the coeval Hoyalacerta (Fig. 2) in the Protosquamata, a more primitive clade than Squamata that includes Squamata and otherwise no extant taxa. O’Connor et al. are mistaken, according to the LRT, when they consider Indrasaurus a scleroglossan squamate.

Antorbital fenestra?
Indrasaurus sister taxa do not have an antorbital fenestra, so the one that appears here (Fg. 1) is suspect, but possible.

FIgure 4. Ornitholestes nests as a sister to Sciurumimus, between Compsognathus and Microraptor.

The STM5-32 specimen of Microraptor (Fig. 3) nests as the basalmost tested Microraptor derived from a sister to Sciurumimus and Ornitholestes (Fig. 4), convergent with and distinct from pre-bird clades. Traditional cladograms, like the recently published Hartman et al. 2019, do not associate these three taxa apart from birds. O’Connor et al. consider Microraptor to be a dromaeosaurid. The LRT rejects that hypothesis of interrelationships.

Three Microraptor species
Since the three tested Microraptors nest apart from one another with high Bootstrap scores, two need to be given new specific names, not lumped under Microraptor zhaoianus, as O’Connor et al. do.

Was Microraptor volant?
O’Connor et al. consider all specimens of Microraptor to be volant (capable of flight). The short, nearly disc-like shape of the coracoid (Fig. 2) argues against this, despite the presence of large feathers in this genus. The key difference between Late Jurassic birds and pre-bird anchiornithids is the elongation of the locked-down coracoid, which marks the genesis of flapping in pterosaurs and birds. Like their ancestor, Ornitholestes, Microraptor had small, disc-like coracoids that slid like those of most tetrapods with coracoids. Based on the elongation and locking down of coracoids, evidently flapping occurred before forelimb elongation in pterosaurs, afterwards in basalmost birds, like the basal Archaeopteryx specimens. Microraptor was a glider at best, not a flapper, which requires locked-down elongate coracoids.

Figure 4. Subset of the LRT focusing on the theropod-bird transition, distinctly different than in Hartman et al. 2019. Here in a fully resolved cladogram, birds and anchiornithids are monophyletic. Taxon inclusion resolves cladistic issues raised by Hartman et al.

I am in the heretical minority
when I say giant azhdarchids and small microraptors were not capable of flight. I report from the evidence, not the feeling, the authority or tradition.

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References
O’Connor et al. (six co-authors) 2019. Microraptor with ingested lizard suggests non-specialized digestive function. Current Biology 29, 1–7. https://doi.org/10.1016/j.cub.2019.06.020